Kodi S. Ravichandran
- BVSc, Madras Veterinary College, Madras, India
- PhD, University of Massachusetts, Amherst, MA
- Postdoc, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Professor and Chair, Microbiology, Immunology, and Cancer Biology
- Phone: 434-243-6093
- Email: Ravi@virginia.edu
- Website: http://med.virginia.edu/faculty/faculty-listing/kr4h/
Apoptotic cell clearance mechanisms in health and disease
Mechanisms Regulating Engulfment of Apoptotic cells,
and Signals Influencing Lymphocyte Development
Our laboratory currently focuses on two major areas.
1. Engulfment of apoptotic cells - the art of eating a good meal.
Everyday we turn over billions of cells as part of normal development and homeostasis. The recognition and phagocytic removal of such cells destined to die (mostly via 'apoptosis') is fundamentally important for our health. Failure to promptly and efficiently clear apoptotic cells can lead to chronic inflammation, autoimmunity and developmental defects. The apoptotic cell clearance is usually done by neighboring cells or by professional phagocytes such as macrophages and dendritic cells.
In studying this process, we consider four broad issues related to 'eating an apoptotic meal'. The first issue is getting to the meal itself. This involves the release of so called 'find-me signals' from apoptotic cells that serve as attraction cues to recruit monocytes and macrophages near an apoptotic cell. We have recently identified a critical for the nucleotides ATP and UTP as find-me signals that are released in a regulated way very early on during apoptosis (Elliott et al. Nature, 2009; Checkeni et al., Nature, 2010 ).
The second issue is determining what is on the menu, and distinguishing the apoptotic cell from the neighboring healthy cells. This is achieved through expression of 'eat-me' signals on apoptotic cells and their recognition by receptors on phagocytes. Here, we focus on the ligands on the dying cell and receptors on phagocytes that are involved in the specific recognition of apoptotic cells. Our recent work has identified a novel type of engulfment receptor (BAI1) that recognizes phosphatidylserine, a key eat-me signal exposed on apoptotic cells (Park et al. Nature 2007, Park et al. Current Biology, 2009).
The third issue is the act of eating the meal itself. Here, we focus on the specific intracellular signals that are initiated within the phagocyte when it comes in contact with apoptotic cells, and how this leads to cytoskeletal rearrangements of the phagocyte and internalization of the target. We have defined the signaling pathway downstream of BAI1 involving the proteins ELMO1, Dock180 and the small GTPase Rac. We have also defined a second signaling module that involves the membrane protein LRP1 and a small intracellular adapter protein GULP. (Gumienny et al. Cell , 2001, Brugnera et al. Nature Cell Biology, 2002; Lu et al. Nature Str Mol. Biol. , 2004; deBakker et al. Currently Biology, 2004; Lu et al. Current Biology , 2005; Ravichandran, Cell, 2003). We have also generated mice with knockout of specific engulfment genes and are currently characterizing them (Elliott et al., Nature, 2010).
The fourth relates to 'after-the-meal' issues. Contrary to other types of phagocytosis (such as bacterial uptake), engulfment of apoptotic cells is 'immunologically silent'. We are interested in determining how apoptotic cells induce an anti-inflammatory state of the phagocyte, and how this relates to immune tolerance (Juncadella et al., Nature, 2013, Mauldin et al., Current Biology, 2013).). Another fun problem in considering one cell eating another is that the phagocyte essentially doubles its cellular contents (including protein, cholesterol, nucleotides etc.). We are addressing how the ingested cargo is processed within the phagocyte, and how the phagocyte manages homeostasis (Kinchen et al. Nature Cell Biology, 2008; Kiss et al. Current Biology, 2007; Ravichandran et al. Nature Rev Immunol. 2007; Kinchen et al, Nature 2010), and how what controls an appetite of the phagocyte in ingesting multiple apoptotic cells (Park et al., Nature, 2011).
The overall goal of these studies is to understand the signaling pathways and the consequences of engulfment at the molecular, cellular and whole organism levels. We use a combination of molecular biology, cell biology, biochemistry, coupled with C.elegans and mouse knockout studies, to gain insights on how specific proteins orchestrate the intracellular signaling during engulfment and lead to the immunologically silent clearance of apoptotic cells. These could have implications for future therapies aimed at limiting inflammation (Elliott et al., Journal of Cell Biol, 2010).
2. Intracellular signaling pathways regulating T and B lymphocyte function.
Our particular focus is on how adapter proteins (which do not have any obvious catalytic activity but mediate protein:protein or protein:lipid interactions) regulate B and T cell development and function. We are addressing how the adapter protein Shc regulates specific checkpoints during T cell development in the thymus, as well as B cell development in the bone marrow. We have generated mice carrying targeted shc1 locus that would allow tissue-specific knockout of Shc expression, and also inducible transgenic mice expressing dominant negative forms of Shc. By disrupting Shc function at different stages of development, we are examining the function of Shc during lymphocyte development and subsequent immune responses in the periphery (Ravichandran et al. Science, 1993; Zhang et al. Nature Immunology, 2002; Trampont et al. Molecular Cell Biology, 2006). We have also been focusing on the role of the chemokine receptor CXCR4 (also a coreceptor for HIV-1) in regulating specific developmental steps during thymic T cell development (Trampont et al. Nature Immunology, 2009).
- Poon I, Chiu Y, Armstrong A, Kinchen J, Juncadella I, Bayliss D, Ravichandran K. Unexpected link between an antibiotic, pannexin channels and apoptosis. Nature. 2014;507(7492): 329-34. PMID: 24646995 | PMCID: PMC4078991
- Hochreiter-Hufford A, Lee C, Kinchen J, Sokolowski J, Arandjelovic S, Call J, Klibanov A, Yan Z, Mandell J, Ravichandran K. Phosphatidylserine receptor BAI1 and apoptotic cells as new promoters of myoblast fusion. Nature. 2013;497(7448): 263-7. PMID: 23615608 | PMCID: PMC3773542
- Juncadella I, Kadl A, Sharma A, Shim Y, Hochreiter-Hufford A, Borish L, Ravichandran K. Apoptotic cell clearance by bronchial epithelial cells critically influences airway inflammation. Nature. 2012. PMID: 23235830 | PMCID: PMC3662023
- Park D, Han C, Elliott M, Kinchen J, Trampont P, Das S, Collins S, Lysiak J, Hoehn K, Ravichandran K. Continued clearance of apoptotic cells critically depends on the phagocyte Ucp2 protein. Nature. 2011;477(7363): 220-4. PMID: 21857682 | PMCID: PMC3513690
- Chekeni F, Elliott M, Sandilos J, Walk S, Kinchen J, Lazarowski E, Armstrong A, Penuela S, Laird D, Salvesen G, Isakson B, Bayliss D, Ravichandran K. Pannexin 1 channels mediate 'find-me' signal release and membrane permeability during apoptosis. Nature. 2010;467(7317): 863-7. PMID: 20944749 | PMCID: PMC3006164
- Elliott M, Zheng S, Park D, Woodson R, Reardon M, Juncadella I, Kinchen J, Zhang J, Lysiak J, Ravichandran K. Unexpected requirement for ELMO1 in clearance of apoptotic germ cells in vivo. Nature. 2010;467(7313): 333-7. PMID: 20844538 | PMCID: PMC3773546
- Kinchen J, Ravichandran K. Identification of two evolutionarily conserved genes regulating processing of engulfed apoptotic cells. Nature. 2010;464(7289): 778-82. PMID: 20305638 | PMCID: PMC2901565
- Elliott M, Chekeni F, Trampont P, Lazarowski E, Kadl A, Walk S, Park D, Woodson R, Ostankovich M, Sharma P, Lysiak J, Harden T, Leitinger N, Ravichandran K. Nucleotides released by apoptotic cells act as a find-me signal to promote phagocytic clearance. Nature. 2009;461(7261): 282-6. PMID: 19741708 | PMCID: PMC2851546
- Trampont P, Tosello-Trampont A, Shen Y, Duley A, Sutherland A, Bender T, Littman D, Ravichandran K. CXCR4 acts as a costimulator during thymic beta-selection. Nature immunology. 2009;11(2): 162-70. PMID: 20010845 | PMCID: PMC2808461
- Kinchen J, Doukoumetzidis K, Almendinger J, Stergiou L, Tosello-Trampont A, Sifri C, Hengartner M, Ravichandran K. A pathway for phagosome maturation during engulfment of apoptotic cells. Nature cell biology. 2008;10(5): 556-66. PMID: 18425118 | PMCID: PMC2851549
- Park D, Tosello-Trampont A, Elliott M, Lu M, Haney L, Ma Z, Klibanov A, Mandell J, Ravichandran K. BAI1 is an engulfment receptor for apoptotic cells upstream of the ELMO/Dock180/Rac module. Nature. 2007;450(7168): 430-4. PMID: 17960134
- Stites E, Trampont P, Ma Z, Ravichandran K. Network analysis of oncogenic Ras activation in cancer. Science (New York, N.Y.). 2007;318(5849): 463-7. PMID: 17947584
- Lu M, Kinchen J, Rossman K, Grimsley C, deBakker C, Brugnera E, Tosello-Trampont A, Haney L, Klingele D, Sondek J, Hengartner M, Ravichandran K. PH domain of ELMO functions in trans to regulate Rac activation via Dock180. Nature structural & molecular biology. 2004;11(8): 756-62. PMID: 15247908
- Brugnera E, Haney L, Grimsley C, Lu M, Walk S, Tosello-Trampont A, Macara I, Madhani H, Fink G, Ravichandran K. Unconventional Rac-GEF activity is mediated through the Dock180-ELMO complex. Nature cell biology. 2002;4(8): 574-82. PMID: 12134158
- Zhang L, Camerini V, Bender T, Ravichandran K. A nonredundant role for the adapter protein Shc in thymic T cell development. Nature immunology. 2002;3(8): 749-55. PMID: 12101399
- Gumienny T, Brugnera E, Tosello-Trampont A, Kinchen J, Haney L, Nishiwaki K, Walk S, Nemergut M, Macara I, Francis R, Schedl T, Qin Y, Van Aelst L, Hengartner M, Ravichandran K. CED-12/ELMO, a novel member of the CrkII/Dock180/Rac pathway, is required for phagocytosis and cell migration. Cell. 2001;107(1): 27-41. PMID: 11595183